bioroebe 0.10.80 → 0.12.24

data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb

@@ -23,6 +23,7 @@ module Bioroebe
   #
   #   Bioroebe.return_fasta_subsection_of_this_file("foobar.fa")
   #   Bioroebe.return_fasta_subsection_of_this_file("foobar.fa", :keep_it_flat)
+  #   Bioroebe.return_fasta_subsection_of_this_file("/home/Temp/bioroebe/fasta/alu_elements.fasta", :keep_it_flat)
   #
   # ========================================================================= #
   def self.return_fasta_subsection_of_this_file(
@@ -42,6 +43,8 @@ module Bioroebe
     end
     if File.exist? i
       dataset = File.readlines(i)
+pp 'DEBUG'
+pp dataset
       inner_array = []
       size = dataset.size
       dataset.each_with_index {|line, index|
@@ -55,16 +58,22 @@ module Bioroebe
           end
           inner_array.prepend(line)
         else
+          # ================================================================= #
           # This will be a FASTA body section.
+          # ================================================================= #
           case extra_options
-          when :keep_body_together # the default
+          # ================================================================= #
+          # === :keep_body_together
+          # ================================================================= #
+          when :keep_body_together, # the default
+               :keep_it_flat
             inner_array << line
           else
             # =============================================================== #
             # Else we have to append it.
             # =============================================================== #
             previous_line = inner_array.last
-            if previous_line.start_with? '>'
+            if previous_line and previous_line.start_with?('>')
               inner_array << line
             else
               inner_array.last.strip!

data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb

@@ -86,17 +86,6 @@ class ShowFastaHeaders < Bioroebe::CommandlineApplication # === Biroebe::ShowFas
     @input
   end
 
-  # ========================================================================= #
-  # === report_this_header_from_that_file
-  # ========================================================================= #
-  def report_this_header_from_that_file(header, file)
-    if @be_verbose
-      erev "The file at #{sfile(file)}#{rev} has the following FASTA header:"
-      e
-    end
-    e "  #{simp(header)}"
-  end
-
   # ========================================================================= #
   # === input_without_extension
   # ========================================================================= #
@@ -116,13 +105,39 @@ class ShowFastaHeaders < Bioroebe::CommandlineApplication # === Biroebe::ShowFas
     }
   end
 
+  # ========================================================================= #
+  # === report_this_header_from_that_file
+  # ========================================================================= #
+  def report_this_header_from_that_file(header, file)
+    if @be_verbose
+      erev "The file at #{sfile(file)}#{rev} has the following FASTA header:"
+      e
+    end
+    e "  #{simp(header)}"
+    if header.include? '|'
+      splitted = header.split('|')
+      if splitted.size > 2
+        assumed_name_of_the_organism = splitted[2].strip
+        if assumed_name_of_the_organism.include? 'OS='
+          assumed_name_of_the_organism = assumed_name_of_the_organism.scan(/ OS=(.+)/).flatten
+          assumed_name_of_the_organism = assumed_name_of_the_organism.first
+          if assumed_name_of_the_organism.include? ' ('
+            assumed_name_of_the_organism = assumed_name_of_the_organism.split(' (').first
+          end
+        end
+        erev 'The organism may be: '+
+             steelblue(assumed_name_of_the_organism)+rev
+      end
+    end
+  end
+
   # ========================================================================= #
   # === run                                                         (run tag)
   # ========================================================================= #
   def run
     files = Dir[input?]
     if files.empty?
-      opnn; e 'No files could be found for '+input?+'.'
+      opnn; e "No files could be found for #{input?}."
     else
       report_these_files(files)
     end

data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb

@@ -29,11 +29,6 @@ class SimplifyFastaHeader < ::Bioroebe::CommandlineApplication # === Bioroebe::S
 
   require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -53,6 +48,7 @@ class SimplifyFastaHeader < ::Bioroebe::CommandlineApplication # === Bioroebe::S
   # ========================================================================= #
   def reset
     super()
+    infer_the_namespace
   end
 
   # ========================================================================= #

data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb

@@ -8,11 +8,6 @@ module Bioroebe
 
 class SplitThisFastaFileIntoChromosomes < ::Bioroebe::CommandlineApplication # === Bioroebe::SplitThisFastaFileIntoChromosomes
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === ALLOWED_CHARACTERS
   #

data/lib/bioroebe/genome/README.md

@@ -0,0 +1,4 @@
+This directory was created on the 12.07.2022.
+
+The idea is that we can make use of class Bioroebe::Genome
+to represent a genome.

data/lib/bioroebe/genome/genome.rb

@@ -0,0 +1,130 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::Genome
+#
+# This class should be able to represent a genome.
+#
+# Usage example:
+#
+#   Bioroebe::Genome.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/genome/genome.rb'
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class Genome < ::Bioroebe::CommandlineApplication # === Bioroebe::Genome
+
+  require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = nil,
+      run_already           = true
+    )
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    infer_the_namespace
+    # ======================================================================= #
+    # All CDS shall be denoted here.
+    # ======================================================================= #
+    @internal_hash[:CDS] = []
+  end
+
+  # ========================================================================= #
+  # === add_the_lac_operon
+  #
+  # If glucose is present and lactose is absent then no transcription
+  # of the lac operon occurs.
+  # ========================================================================= #
+  def add_the_lac_operon
+    @internal_hash[:lac_operon] = true
+  end
+
+  # ========================================================================= #
+  # === is_the_lac_operon_transcribable?
+  # ========================================================================= #
+  def is_the_lac_operon_transcribable?
+    if !lactose_is_present?
+      return false
+    elsif glucose_is_present? and lactose_is_present?
+      return false
+    elsif glucose_is_present?
+      return true
+    else
+      return false
+    end
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    # add_the_lac_operon
+    first = first?
+    if first and File.exist?(first)
+      _ = Bioroebe.parse_fasta(first)
+      @internal_hash[:full_sequence] = _.sequence?
+      annotate(
+        [
+          [2931, 3917]
+        ]
+      ) # This is for the phage.
+pp self
+pp all_genes?
+    end
+  end
+
+  # ========================================================================= #
+  # === all_genes?
+  #
+  # This method will return all genes.
+  # ========================================================================= #
+  def all_genes?
+    result = []
+    _ = @internal_hash[:full_sequence]
+    @internal_hash[:CDS].map {|start_nucleotide, end_nucleotide|
+      result << _[start_nucleotide - 1, (end_nucleotide - start_nucleotide) + 1]
+    }
+    return result
+  end
+
+  # ========================================================================= #
+  # === annotate
+  #
+  # Annotate some genes here, or rather CDS.
+  # ========================================================================= #
+  def annotate(array)
+    array.each {|this_array|
+      @internal_hash[:CDS] << [this_array.first, this_array.last]
+    }
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::Genome[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::Genome.new(ARGV)
+end # bioroebe_genome

data/lib/bioroebe/genomes/genome_pattern.rb

@@ -28,11 +28,6 @@ class GenomePattern < ::Bioroebe::CommandlineApplication # === Bioroebe::GenomeP
 
   require 'bioroebe/gene/gene.rb'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -50,15 +45,14 @@ class GenomePattern < ::Bioroebe::CommandlineApplication # === Bioroebe::GenomeP
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @hash
     # ======================================================================= #
     @hash = {}
+    # === :array_genes
     @hash[:array_genes] = []
+    # === :be_verbose
     @hash[:be_verbose] = true # If true then we tell the user what we will do.
   end
 

data/lib/bioroebe/gui/gtk

@@ -0,0 +1 @@
+gtk3

data/lib/bioroebe/gui/gtk3/alignment/alignment.rb

@@ -17,47 +17,40 @@ module GUI
 
 module Gtk
 
-class Alignment < ::Gtk::Box # === Bioroebe::GUI::Gtk::Alignment 
+class Alignment < ::Gtk::BaseModuleBox # === Bioroebe::GUI::Gtk::Alignment 
 
-  require 'bioroebe/sequence/alignment.rb'
+  require 'bioroebe/gui/shared_code/alignment/alignment_module.rb'
+  include Bioroebe::GUI::AlignmentModule
 
   require 'bioroebe/constants/GUIs.rb'
   include ::Bioroebe::GUI
 
-  require 'gtk_paradise/requires/require_the_base_module.rb'
-  include ::Gtk::BaseModule
-
   # ========================================================================= #
-  # === NAMESPACE
+  # === TOOLTIP_HINT_FOR_THE_DO_ANALYSE_BUTTON
   # ========================================================================= #
-  NAMESPACE = inspect
+  TOOLTIP_HINT_FOR_THE_DO_ANALYSE_BUTTON =
+    "Click on this button to analyse the given sequence. Make sure "\
+    "to use <b>newlines</b> in order to split the sequence at hand."
 
   # ========================================================================= #
-  # === TITLE
-  # ========================================================================= #
-  TITLE = 'Alignment'
-
-  # ========================================================================= #
-  # === WIDTH
-  # ========================================================================= #
-  WIDTH = '60%'
-
-  # ========================================================================= #
-  # === HEIGHT
-  # ========================================================================= #
-  HEIGHT = '50%'
-
-  # ========================================================================= #
-  # === USE_THIS_FONT
+  # === TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE
+  #
+  # This is the base-tooltip for the entry that retains our consensus
+  # sequence.
   # ========================================================================= #
-  USE_THIS_FONT = :dejavu_condensed_22
+  TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE = 
+    'This entry will contain the <b>consensus sequence</b>, '\
+    'derived from the above sequences.'
 
   # ========================================================================= #
-  # === FONT_FOR_THE_ENTRIES
-  #
-  # The entries must use a mono-spaced font.
+  # === TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION
   # ========================================================================= #
-  FONT_FOR_THE_ENTRIES = :hack_20
+  TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION = 
+    "\n\nTake note that in the event that there is <b>an even number of "\
+    "input sequences</b>, the entries defined before will take precedence. "\
+    "So, for instance, if you have four sequences in total, where two are "\
+    "ATTA and the next two are ATTT, then the consensus sequence is "\
+    "currently assumed to be <b>ATTA</b>."
 
   # ========================================================================= #
   # === initialize
@@ -79,18 +72,16 @@ class Alignment < ::Gtk::Box # === Bioroebe::GUI::Gtk::Alignment
   # ========================================================================= #
   def reset
     reset_the_internal_variables
+    infer_the_namespace
     # ======================================================================= #
     # === @configuration
     # ======================================================================= #
-    @configuration = [true, __dir__, NAMESPACE]
+    @configuration = [true, __dir__, namespace?]
     title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
     use_gtk_paradise_project_css_file
     append_project_CSS_file 
     infer_the_size_automatically
-    # ======================================================================= #
-    # === @alignment
-    # ======================================================================= #
-    @alignment = Bioroebe::Alignment.new(nil, :do_not_run_yet)
+    reset_the_alignment_object
   end
 
   # ========================================================================= #
@@ -114,10 +105,10 @@ class Alignment < ::Gtk::Box # === Bioroebe::GUI::Gtk::Alignment
     # ======================================================================= #
     # === @scrolled_window
     # ======================================================================= #
-    @scrolled_window = gtk_scrolled_window(@text_view)
+    @scrolled_window = create_scrolled_window(@text_view)
     @scrolled_window.width_height(300, 400)
-    @scrolled_window.css_class('pad4px')
-    @scrolled_window.bblack1
+    @scrolled_window.pad4px
+    @scrolled_window.bblack2
   end
 
   # ========================================================================= #
@@ -127,39 +118,13 @@ class Alignment < ::Gtk::Box # === Bioroebe::GUI::Gtk::Alignment
     # ======================================================================= #
     # === @text_buffer
     # ======================================================================= #
-    @text_buffer = gtk_text_buffer
+    @text_buffer = create_text_buffer
     # ======================================================================= #
     # === @text_view
     # ======================================================================= #
-    @text_view = gtk_text_view(@text_buffer)
+    @text_view = create_text_view(@text_buffer)
   end
 
-  # ========================================================================= #
-  # === text_view_widget?
-  # ========================================================================= #
-  def text_view_widget?
-    @text_view
-  end
-
-  # ========================================================================= #
-  # === do_analyse
-  # ========================================================================= #
-  def do_analyse(
-      _ = @text_buffer.text?
-    )
-    if _ and !_.empty?
-      _.strip!
-      @alignment.use_this_as_input(_)
-      consensus_sequence = @alignment.consensus_sequence?
-      @entry_consensus_sequence.set_text(consensus_sequence)
-    else
-      pop_up_widget(
-        over_this_widget: text_view_widget?,
-        text:             'Please assign a sequence first.'
-      )
-    end
-  end; alias do_analyse_again do_analyse # === do_analyse_again
-
   # ========================================================================= #
   # === create_the_entries                           (entry tag, entries tag)
   # ========================================================================= #
@@ -173,49 +138,18 @@ class Alignment < ::Gtk::Box # === Bioroebe::GUI::Gtk::Alignment
     @entry_consensus_sequence.use_this_font = FONT_FOR_THE_ENTRIES
     @entry_consensus_sequence.yellow_background
     update_the_hint_for_the_entry_consequences_sequence(
-      'This entry will contain the consensus sequence, '\
-      'derived from the above sequences.'
+      TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE+
+      TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION
     )
     # ======================================================================= #
     # === @entry_numbers
     # ======================================================================= #
-    @entry_numbers = gtk_entry
+    @entry_numbers = create_entry
+    @entry_numbers.bblack1
     @entry_numbers.use_this_font = FONT_FOR_THE_ENTRIES
     @entry_numbers.hint = 'This area may indicate the numbers for '\
                           'the alignment shown right above.'
-  end
-
-  # ========================================================================= #
-  # === realign_the_numbers_showing_how_long_the_consensus_sequence_is
-  # ========================================================================= #
-  def realign_the_numbers_showing_how_long_the_consensus_sequence_is
-    @entry_numbers.center
-    n_characters = @entry_consensus_sequence.text?.size
-    @entry_numbers.set_text(return_fill_up_to(n_characters))
-  end
-
-  # ========================================================================= #
-  # === return_fill_up_to
-  # ========================================================================= #
-  def return_fill_up_to(i)
-    _ = ''.dup
-    i.times {|counter|
-      counter = (counter+1) % 10
-      _ << counter.to_s
-    }
-    return _
-  end
-
-  # ========================================================================= #
-  # === connect_skeleton                                        (connect tag)
-  # ========================================================================= #
-  def connect_skeleton
-    abort_on_exception
-    minimal(return_the_first_row,                 5)
-    minimal(@scrolled_window,          2)
-    minimal(@button_do_analyse,        2)
-    minimal(@entry_consensus_sequence, 2)
-    minimal(@entry_numbers,            2)
+    @entry_numbers.very_light_yellow_background
   end
 
   # ========================================================================= #
@@ -223,12 +157,12 @@ class Alignment < ::Gtk::Box # === Bioroebe::GUI::Gtk::Alignment
   # ========================================================================= #
   def return_the_first_row
     _ = gtk_hbox
-    top_label = gtk_left_aligned_label(
-      'Input the sequences that you wish to compare to one another'
+    top_label = left_aligned_label(
+      TEXT_INPUT_THE_SEQUENCES
     )
     top_label.center
     _.minimal(top_label)
-    event_box = gtk_event_box(
+    event_box = event_box(
       image_document_open
     )
     event_box.hint = 'Click on this icon to open a local file.'
@@ -249,22 +183,6 @@ class Alignment < ::Gtk::Box # === Bioroebe::GUI::Gtk::Alignment
     create_the_scrolled_window
   end
 
-  # ========================================================================= #
-  # === update_the_hint_for_the_entry_consequences_sequence
-  # ========================================================================= #
-  def update_the_hint_for_the_entry_consequences_sequence(
-      i = ''
-    )
-    @entry_consensus_sequence.hint = i
-  end
-
-  # ========================================================================= #
-  # === run                                                         (run tag)
-  # ========================================================================= #
-  def run
-    create_skeleton_then_connect_skeleton
-  end
-
   # ========================================================================= #
   # === create_the_buttons                                      (buttons tag)
   # ========================================================================= #
@@ -273,11 +191,10 @@ class Alignment < ::Gtk::Box # === Bioroebe::GUI::Gtk::Alignment
     # === @button_do_analyse
     # ======================================================================= #
     @button_do_analyse = bold_button('_Do analyse')
+    @button_do_analyse.clear_background
     @button_do_analyse.bblack1
     @button_do_analyse.on_hover(:lightblue)
-    @button_do_analyse.hint = 'Click on this button to '\
-      'analyse the given sequence. Make sure to use '\
-      'newlines in order to split the sequence at hand.'
+    @button_do_analyse.hint = TOOLTIP_HINT_FOR_THE_DO_ANALYSE_BUTTON
     @button_do_analyse.on_clicked {
       do_analyse
       realign_the_numbers_showing_how_long_the_consensus_sequence_is
@@ -288,26 +205,13 @@ class Alignment < ::Gtk::Box # === Bioroebe::GUI::Gtk::Alignment
           (@text_buffer.text?.count("\n")+1).to_s+" sequences.\n\nNote "\
           "that only the minimal length will be compared - "\
           "superfluous nucleotides will NOT be considered unless "\
-          "they can be aligned to other sequences."
+          "they can be aligned to other sequences."+
+          TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION
         ).squeeze(' ')
       )
     }
   end
 
-  # ========================================================================= #
-  # === Bioroebe::GUI::Gtk::Alignment.run
-  # ========================================================================= #
-  def self.run(
-      i = ARGV
-    )
-    require 'gtk_paradise/run'
-    _ = ::Bioroebe::GUI::Gtk::Alignment.new(i)
-    r = ::Gtk.run
-    r << _
-    r.automatic_size_then_automatic_title
-    r.top_left_then_run
-  end
-
   # ========================================================================= #
   # === do_open_and_assign_a_local_file
   # ========================================================================= #
@@ -330,6 +234,71 @@ class Alignment < ::Gtk::Box # === Bioroebe::GUI::Gtk::Alignment
     end
   end
 
+  # ========================================================================= #
+  # === connect_skeleton                                        (connect tag)
+  # ========================================================================= #
+  def connect_skeleton
+    abort_on_exception
+    grid = default_grid
+    grid.full_row(return_the_first_row)
+    grid.full_row(@scrolled_window)
+    grid.full_row(@entry_consensus_sequence)
+    grid.full_row(@entry_numbers)
+    grid.full_row(@button_do_analyse)
+    grid.hcenter
+    maximal(grid)
+  end
+
+  # ========================================================================= #
+  # === do_analyse
+  #
+  # This method will be called whenever the user hits the "Do analyse"
+  # button.
+  # ========================================================================= #
+  def do_analyse(
+      _ = @text_buffer.text?
+    )
+    if _ and !_.empty?
+      _.strip!
+      @alignment.use_this_as_input(_)
+      consensus_sequence = return_the_consensus_sequence
+      @entry_consensus_sequence.set_text(consensus_sequence)
+    else
+      pop_up_widget(
+        over_this_widget: text_view_widget?,
+        text:             'Please assign a sequence first.'
+      )
+    end
+  end; alias do_analyse_again do_analyse # === do_analyse_again
+
+  # ========================================================================= #
+  # === update_the_hint_for_the_entry_consequences_sequence
+  # ========================================================================= #
+  def update_the_hint_for_the_entry_consequences_sequence(
+      i = ''
+    )
+    @entry_consensus_sequence.hint = i
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    super()
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::Alignment.run
+  # ========================================================================= #
+  def self.run(
+      i = ARGV
+    )
+    require 'gtk_paradise/run'
+    r = ::Gtk.run
+    r << ::Bioroebe::GUI::Gtk::Alignment.new(i)
+    r.automatic_top_left_then_run
+  end
+
 end; end; end; end
 
 if __FILE__ == $PROGRAM_NAME